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The former chief of licensing for the drug giant Pfizer has stepped in as CEO of Karuna Pharmaceuticals, a stealthy Boston startup focused on new treatments for schizophrenia. Ed Harrigan tells me that he started the job at Karuna this month.

Karuna has two novel programs in development for the treatment of schizophrenia, Harrigan says. Karuna has been incubating at the Boston firm PureTech Ventures, whose partner Eric Elenko had been in charge of day-to-day operations before Harrigan took over those duties. Karuna’s founding team also includes PureTech associate Andrew Miller.

Both Elenko and Harrigan declined to reveal any specifics about the science at the startup, yet they did mention that one of the firm’s molecules with a novel mechanism for treating schizophrenia is being tested in humans. Schizophrenia, which affects about 2.4 million American adults, is a mental disorder that impacts people’s ability to tell what is real and not real.

Harrigan, 57, is a neurologist by training whose name gives Karuna lots of credibility in the pharmaceutical world. Before he left Pfizer (NYSE: PFE) in March 2010, Harrigan led the $1 billion deal between the company and Bristol-Myers Squibb (NYSE: BMY) that brought Pfizer commercial rights to Bristol-Myers’s blood thinner apixaban. The companies are seeking FDA approval of apixaban, which could be a blockbuster drug for the firms. Earlier in his career at Pfizer, Harrigan also played a key role in the development of the antipsychotic pill ziprasidone (Geodon).

At Karuna, Harrigan is trying to develop innovative medicines for a market now dominated by industry heavyweights. Some of the leading drugs for schizophrenia today include Eli Lilly’s (NYSE: LLY) olanzapine (Zyprexa), Bristol-Myers and Otsuka’s aripiprazole (Abilify) and AstraZeneca’s quetiapine (Seroquel). Yet none of these drugs are perfect, and Karuna’s new CEO says he believes there are opportunities for treatments with novel mechanisms to improve the lives of patients.

The startup’s lead drug is already making progress, Harrigan says. “We have clinical evidence in the target population that, using the standard measurement for symptoms of psychosis in patients with schizophrenia, there is significant improvement,” the CEO says. He declined to offer a timeline for the drug’s development.

Harrigan follows several Pfizer vets who have taken leading roles at PureTech-backed biotechs or the venture firm itself. His former Pfizer colleague, Jeffrey Ives, is chief executive of Cambridge, MA-based Satori Pharmaceuticals, which was hatched at PureTech to develop drugs for Alzheimer’s disease. And former Pfizer R&D chief John LaMattina joined PureTech as a senior partner in late 2009.

In true PureTech fashion, Karuna is building a team with top names in pharma and academia. Steven Paul, former president of research at Lilly, is the startup’s chairman and a scientific advisor. The firm’s scientific advisory board also includes Joseph Coyle, a professor of psychiatry at Harvard Medical School; Jeffrey Conn, a professor of pharmacology and director of the drug discovery program at Vanderbilt; Anthony Grace, a professor of neuroscience, psychiatry, and psychology at the University of Pittsburgh; and Carol Tamminga, a psychiatric researcher at the University of Texas Southwestern.

For now, Karuna is operating with the support of PureTech and hasn’t raised money from outside investors, according to Elenko, who notes that there has been a lot of interest in the startup. Though technically based in PureTech’s offices, Karuna is largely a virtual operation. Its CEO, Harrigan, is still living in the New London, CT, area and the company is using contract research facilities and talent rather than running its own labs. Harrigan says he is now the firm’s only full-time employee.

We’ll provide more details on Karuna once we learn more about the firm’s science and its plans for clinical trials.